About 20 family members of the victims were sitting in the public gallery, alongside Leanne Lucas, a yoga instructor who was also stabbed in the attack.
Mr Justice Julian Goose told the court the defendant had “chosen” not to say anything and ordered a further preparatory hearing ahead of the trial to take place in December.
As he remanded him in custody, he addressed Mr Rudakubana directly.
He said: “Mr Rudakubana can you hear me? Just raise your hand if you can hear me.”
The defendant did not respond.
As he remanded him in custody, the judge added: “Well I know you can hear me because the officer behind you said I can be heard.”
The defendant, of Old School Close in Banks, is charged with three counts of murder, 10 of attempted murder, possession of a knife, production of biological toxin, ricin, and possession of information likely to be useful to a person committing or preparing to commit an act of terrorism.
The attempted murder charges relate to eight children, who cannot be named for legal reasons, Ms Lucas and businessman John Hayes.
Mr Rudakubana is next due to appear at Liverpool Crown Court on 12 December, with a trial set for 20 January, which is estimated to last four to six weeks.
